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- PDB-2hpr: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR MUTANT WITH MET 5... -

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Basic information

Entry
Database: PDB / ID: 2hpr
TitleHISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR MUTANT WITH MET 51 REPLACED BY VAL AND SER 83 REPLACED BY CYS (M51V, S83C)
ComponentsHISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


regulation of carbohydrate utilization / phosphoenolpyruvate-dependent sugar phosphotransferase system / cytoplasm
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHerzberg, O.
Citation
Journal: Structure / Year: 1994
Title: Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.
Authors: Liao, D.I. / Herzberg, O.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Structure of the Histidine-Containing Phosphocarrier Protein Hpr from Bacillus Subtilis at 2.0-Angstroms Resolution
Authors: Herzberg, O. / Reddy, P. / Sutrina, S. / Saier Junior, M.H. / Reizer, J. / Kapadia, G.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of the Bacillus Subtilis Histidine-Containing Phosphocarrier Protein Hpr and Some of its Site-Directed Mutants
Authors: Kapadia, G. / Reizer, J. / Sutrina, S. / Saier Junior, M.H. / Reddy, P. / Herzberg, O.
History
DepositionSep 9, 1992Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1632
Polymers9,0671
Non-polymers961
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
hetero molecules

A: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3264
Polymers18,1342
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1020 Å2
ΔGint-34 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.260, 47.260, 61.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-200-

HOH

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Components

#1: Protein HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Mass: 9067.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / References: UniProt: P08877
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE SPECIFICATIONS ARE BASED ON THE USE OF DSSP OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICATIONS ARE BASED ON THE USE OF DSSP OF W. KABSCH AND C. SANDER (BIOPOLYMERS, V. 22, P. 2577, 1983).
Has protein modificationY
Sequence detailsTHE WILD-TYPE PROTEIN HAS 88 AMINO ACID RESIDUES. THE STRUCTURE PRESENTED IN THIS ENTRY IS OF AN ...THE WILD-TYPE PROTEIN HAS 88 AMINO ACID RESIDUES. THE STRUCTURE PRESENTED IN THIS ENTRY IS OF AN ENGINEERED PROTEIN IN WHICH SER 83 HAS BEEN REPLACED BY CYS. THE FIRST AMINO ACID RESIDUE (MET) HAS BEEN PROCESSED. RESIDUE 51 IS A VAL RATHER THAN THE MET FOUND IN THE NATURAL SEQUENCE. THE PROTEIN IS FULLY ACTIVE IN THE PTS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 6.4 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
30.5 %(w/v)PEG10001reservoir
4100 mMcitrate1reservoir
568 %satammonium sulfate1reservoir
1protein1drop
21dropNaCl

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 5083 / % possible obs: 90 % / Rmerge F obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 58 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.145 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 5 99 730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.041
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 4496 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.8 Å2

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